The purpose of this study was to show the normal sonographic embryologic anatomy of the cisterna magna septa, fourth ventricle, and cerebellar vallecula at various stages of development and our experience with their variable appearance in multiple planes and to discuss the probable relationship between the cisterna magna septa, Dandy-Walker continuum, mega cisterna magna, and persistent Blake's pouch. Retrospective and prospective selection of examples of cisterna magna septa was performed over approximately a 12-month period. Standard and nonstandard imaging planes were adopted as necessary. The septa are typically seen inferoposterior to the cerebellar vermis, usually straight and parallel, arising at the cerebellovermian angle and coursing posteriorly to the occipital bone. The cisterna magna septa become contiguous with the roof of the fourth ventricle inferior to the cerebellar vermis. The cerebrospinal fluid space enclosed between the cisterna magna septa is in direct contiguity with the fourth ventricle via the vallecula and is always completely anechoic because it develops intra- and not extra-axially. We propose that the cisterna magna septa represent the walls of Blake's pouch, a phylogenetic vestigial structure observed during ontogeny. Additionally, our observations support current opinion that a persistent Blake's pouch and mega cisterna magna represent (less severe) abnormalities within the Dandy-Walker continuum. The cisterna magna septa therefore are a marker of normal development of the roof of the rhombencephalon. Deviation from their normal appearances should prompt a closer assessment for associated abnormalities of the cerebellum, vermis, and brain stem by additional imaging in orthogonal planes with either sonography or magnetic resonance imaging.